I think the solution which you have mentioned is good if you remove the
if condition in the for block as you have already taken care of it
outside the for block.

Anyways, You can do this in two ways
1)
if (param == true) {
  x = vector1
  y = vector2
}else {
  x = vector2
  y = vector1
}
for (x, index i)
  for (y, index j)
       myObject o = new myObject(x.elementAt(i), y.elementAt(j))

2)
for (vector1, index i)
  for (vector2, index j)
     if (param == true)
        myObject o = new myObject(vector1.elementAt(i),
vector2.elementAt(j))
     else
        myObject o = new myObject(vector2.elementAt(i),
vector1.elementAt(j))

I think first one is better because of less number of comparisions
(even though you are using two extra variables).